Stretching of a single-stranded DNA: Evidence for structural transition

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.Comment: 10 pages, 4 figure

Does changing the pulling direction give better insight into biomolecules?

Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different phase diagrams. The simple model proposed here indicates that in one case the system undergoes a transition akin to the unzipping of a $\beta$ sheet, while in the other case the transition is of a shearing (slippage) nature. Our results are qualitatively similar to experimental results. This demonstrates the importance of varying the pulling direction since this may yield enhanced insights into the molecular interactions responsible for the stability of biomolecules.Comment: RevTeX v4, 10 pages with 6 eps figure

Spin-glass-like state in GdCu: role of phase separation and magnetic frustration

We report investigations on the ground state magnetic properties of intermetallic compound GdCu through dc magnetization measurements. GdCu undergoes first order martensitic type structural transition over a wide temperature window of coexisting phases. The high temperature cubic and the low temperature orthorhombic phases have different magnetic character and they show antiferromagnetic and helimagnetic orderings below 145 K and 45 K respectively. We observe clear signature of a glassy magnetic phase below the helimagnetic ordering temperature, which is marked by thermomagnetic irreversibility, aging and memory effects. The glassy magnetic phase in GdCu is found to be rather intriguing with its origin lies in the interfacial frustration due to distinct magnetic character of the coexisting phases.Comment: Physical Review B 83, 134427 (2011

Intermodal entanglement in Raman processes

The operator solution of a completely quantum mechanical Hamiltonian of the Raman processes is used here to investigate the possibility of obtaining intermodal entanglement between different modes involved in the Raman processes (e.g. pump mode, Stokes mode, vibration (phonon) mode and anti-Stokes mode). Intermodal entanglement is reported between a) pump mode and anti-Stokes mode, b) pump mode and vibration (phonon) mode c) Stokes mode and vibration phonon mode, d) Stokes mode and anti-stokes mode in the stimulated Raman processes for the variation of the phase angle of complex eigenvalue $\alpha_{1}$ of pump mode $a$. Some incidents of intermodal entanglement in the spontaneous and the partially spontaneous Raman processes are also reported. Further it is shown that the specific choice of coupling constants may produce genuine entanglement among Stokes mode, anti-Stokes mode and vibration-phonon mode. It is also shown that the two mode entanglement not identified by Duan's criterion may be identified by Hillery-Zubairy criteria. It is further shown that intermodal entanglement, intermodal antibunching and intermodal squeezing are independent phenomena.Comment: 11 pages, 4 figure

Problems Affecting Labor

Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by ℙ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G A (a 3-α helix fold) and G B (an α/β fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G A domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G Bs, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed

Manufacturer's pricing strategies in cooperative and non-cooperative advertising supply chain under retail competition

This article studies the manufacturer's pricing strategy in a supply chain with a single manufacturer and two competing retailers. The manufacturer, as a Stackelberg leader specifies wholesale prices to two retailers who face advertisement dependent demand. Based on this gaming structure, two mathematical models are developed - the cooperative advertising model where manufacturer shares a fraction of retailers' advertising costs and the non-cooperative advertising model where manufacturer does not share any retailer's advertising expenses. The optimal strategies of the manufacturer and retailers are determined and a numerical example is taken to illustrate the theoretical results derived. We show that cooperative advertising policy is beneficial not only for the participating entities but also for the entire supply chain

KSZ tomography and the bispectrum

Several statistics have been proposed for measuring the kSZ effect by combining the small-scale CMB with galaxy surveys. We review five such statistics, and show that they are all mathematically equivalent to the optimal bispectrum estimator of type $\langle ggT \rangle$. Reinterpreting these kSZ statistics as special cases of bispectrum estimation makes many aspects transparent, for example optimally weighting the estimator, or incorporating photometric redshift errors. We analyze the information content of the bispectrum and show that there are two observables: the small-scale galaxy-electron power spectrum $P_{ge}(k_S)$, and the large-scale galaxy-velocity power spectrum $P_{gv}(k)$. The cosmological constraining power of the kSZ arises from its sensitivity to fluctuations on large length scales, where its effective noise level can be much better than galaxy surveys.Comment: 39 page

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure

Force induced triple point for interacting polymers

We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for three different models of mutually attracting but self avoiding polymers are presented. One of these models has an intermediate phase and it shows a triple point but not the others. A general phase diagram with multicritical points in an extended parameter space is also discussed.Comment: 4 pages, 8 figures, revtex

Structural domain and spin ordering induced glassy magnetic phase in single layered manganite Pr0.22_{0.22}Sr1.78_{1.78}MnO4_4

The single layered manganite Pr$_{0.22}$Sr$_{1.78}$MnO$_4$ undergoes structural transition from high temperature tetragonal phase to low temperature orthorhombic phase below room temperature. The orthorhombic phase was reported to have two structural variants with slightly different lattice parameters and Mn-3$d$ levels show orbital ordering within both the variants, albeit having mutually perpendicular ordering axis. In addition to orbital ordering, the orthorhombic variants also order antiferromagnetically with different N\'eel temperatures. Our magnetic investigation on the polycrystalline sample of Pr$_{0.22}$Sr$_{1.78}$MnO$_4$ shows large thermal hysteresis indicating the first order nature of the tetragonal to orthorhombic transition. We observe magnetic memory, large relaxation, frequency dependent ac susceptbility and aging effects at low temperature, which indicate spin glass like magnetic ground state in the sample. The glassy magnetic state presumably arises from the interfacial frustration of orthorhombic domains with orbital and spin orderings playing crucial role toward the competing magnetic interactions.Comment: 6 pages, 4 figures, Accepted in Europhysics Letter